Leaf images rotated wrong way on Sapling tree Gen
Well depending on what option you picked when you made the leaves for the tree you will have to fix this differently.

For both Rectangular and Hexagonal you will need to edit the UV map for the leaf object.

For the cube leaf the key is to get the stem of the leaf to line up on the bottom of the UVs in the center.
In the case of the Hexagonal leaf you want the bottom point of the hexagon to be right on the stem.

When you have the UVs set up that way the stem of the leaf will be right on the branch. If the leaf is not in the correct orientation from the branch you need to rotate the UVs. Start by rotating the UVs by 90° then see which way you need to go. (A UV Image Editor and 3D view open helps immensely here.)



For the DupliVert or DupliFaces options it is easier, you only need to align the origin of the leaf object onto the stem. A picture does a better job of explaining it:

Remember here you are moving the object in edit mode.